Guidelines for database cross references

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 TO BE COMPLETED

We have two types of cross-references in the ontology: (1) Definition database cross-references and (2) General/term database cross-references, also known as 'Mappings' (for example in AmiGO). Guidelines for definition database cross-references can be found in the Guidelines for GO textual definitions page. The present page describes guidelines for general/term database cross-references.

Database cross-references

General database cross-references, or general dbxrefs, are links to external resources. They should be used where a GO term is identical to an object in another database.


Main resources GO links to are:

Aspect Database Prefix in GO (case-sensitive)  Example mapping Notes
 All  Wikipedia  Wikipedia:  Wikipedia:Barr_body  
 Molecular Function  EC  EC:  EC:2.7.7.27  Partial ECs should only be used for grouping classes, for example GO:0016491 oxidoreductase activity maps to EC:1.-.-.-'. Dashes are mandatory.
 KEGG_REACTION  KEGG_REACTION  KEGG_REACTION:R00948  
 MetaCyc  MetaCyc:  MetaCyc:GLUC1PADENYLTRANS-RXN  
 RHEA  RHEA:  RHEA:12120  GO maps to the non-directional reaction
 TCDB TC:  TC:3.A.1.115.1  
 University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) reaction  UM-BBD_reactionID:r0920  
 Biological Process  KEGG_PATHWAY    
 MetaCyc pathway    
 University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) pathway  UM-BBD_pathwayID:tbz     
     
  • EC: Provisional ECs (#.#.#.n#; for e.g., 3.5.1.n3) can be used. When they are turned into real EC numbers they are "transferred", so the new ID is traceable. The permanent EC should be used in GO.
  • RHEA: GO editors can use new (not yet public) RHEA IDs as database cross-references. These are filtered out from the public version of the ontology until they are available. Note that they cannot be used as definition xrefs.
  • Reactome??? these are managed automatically by Reactome, they should not be in the editor's version of the ontology (TBC)

Obsolete database cross-references and obsolete GO terms

  • If a cross reference is deprecated in the source database (for example, a deleted entry in EC, that cross-reference should be removed from GO.
  • If a GO term is obsoleted has a cross-reference to a valid external database entry, then the cross-reference is kept on the obsolete GO term. This situation arises when a term is out of scope for GO but correct in the external database.

Links to enzyme resources

  • Rhea: Expert-curated knowledgebase of chemical and transport reactions of biological interest - and the standard for enzyme and transporter annotation in UniProtKB.
  • Intenz IntEnz (Integrated relational Enzyme database) is a freely available resource focused on enzyme nomenclature. IntEnz is created in collaboration with the Swiss Institute of Bioinformatics (SIB). This collaboration is responsible for the production of the ENZYME resource.
  • Enzyme Commission - IUBMB
  • EC enzyme nomenclature
  • KEGG reactions
  • MetaCyc


Step-by-step instructions

Adding a database cross-reference

  1.  In Protege, navigate to the term to which you wish to add to a database cross references'.
  2.  In the Annotation window on the right, click on the + to the right of Annotations at the very top of the window.
  3.  In the pop-up window that appears, select 'database_cross_reference' in the left hand window, and 'Literal' tab on the right side.
  4. Add cross reference ID and select 'xsd:string' as Datatype.
  5. Click on OK to save your edits.
  6. See Ontology_Editors_Daily_Workflow for commit, push and merge instructions.

Adding a database cross-reference types

Database cross-references may have a type (optional).

  • If the same cross-reference is used on multiple GO terms, then reference type is mandatory. In this case, it is a broadMatch.
  • If a term has more than one cross reference from a source (for example, 2 RHEA database cross references), then reference type is mandatory. In this case, it is a narrowMatch.
  • The db xref types are derived from the W3.org standards. The types of skos:mappingRelation used by GO are: exactMatch, broadMatch, narrowMatch and relatedMatch.
  • To edit a cross-reference type:
    • Click on the @ sign next to the cross-reference.
    • Click on the + sign on the right to add an annotation.
    • Select source in the left-hand menu, and Literal in the right-hand menu. Add the cross-reference type:
      • skos:exactMatch: GO term meaning is exactly the same as the cross-referenced term; single EXACT or RELATED match allowed per term for any xref type
      • skos:broadMatch: GO term meaning is narrower than that of the cross-referenced term. More than one BROAD xref is allowed per term, and BROAD xref can be mapped to multiple terms; need to add this to have multiple RHEA cross refs
      • skos:narrowMatch: GO term meaning is more general than that of the cross-referenced term. More than one NARROW xref is allowed per term, but a given NARROW xref can only be mapped to a single term
      • skos:relatedMatch: GO term meaning is not exactly the same as the cross-referenced term, but the best match; single EXACT or RELATED match allowed per term for any xref type
  • RHEA cross-references are implicitly skos:exactMatch by default. This can be changed by an editor if it is not the case.
  • EC and MetaCyc cross-references have no default type but are not considered exact; if they are exact, type skos:exactMatch should be added for clarity.
  • Only one skos:exactMatch for each cross-reference source is allowed.
  • See Ontology_Editors_Daily_Workflow for commit, push and merge instructions.

Review Status

Last reviewed: March 13, 2024

Reviewed by: Pascale Gaudet


Back to: Ontology editors' manual